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Next-generation sequencing

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https://www.readbyqxmd.com/read/29353449/blastulation-timing-is-associated-with-differential-mitochondrial-content-in-euploid-embryos
#1
Jacqueline R Ho, Nabil Arrach, Katherine Rhodes-Long, Wael Salem, Lynda K McGinnis, Karine Chung, Kristin A Bendikson, Richard J Paulson, Ali Ahmady
PURPOSE: Preimplantation genetic screening (PGS) and assessment of mitochondrial content (MC) are current methods for selection of the best embryos for transfer. Studies suggest that time-lapse morphokinetics (TLM) may also be helpful for selecting embryos more likely to implant. In our study, we sought to examine the relationship between TLM parameters and MC to determine if they could be used adjunctively in embryo selection. We also examined the relationship between MC with ploidy and blastulation...
January 20, 2018: Journal of Assisted Reproduction and Genetics
https://www.readbyqxmd.com/read/29353225/spectrum-of-mutations-in-index-patients-with-familial-hypercholesterolemia-in-singapore-single-center-study
#2
Sharon Li Ting Pek, Sanjaya Dissanayake, Jessie Choi Wan Fong, Michelle Xueqin Lin, Eric Zit Liang Chan, Justin I-Shing Tang, Chee Wan Lee, Hean Yee Ong, Chee Fang Sum, Su Chi Lim, Subramaniam Tavintharan
BACKGROUND AND AIMS: Familial hypercholesterolemia (FH) is an autosomal dominant genetic disease characterized by the presence of high plasma low density lipoproteins cholesterol (LDL-c). Patients with FH, with mutation detected, are at increased risk of premature cardiovascular disease compared to those without mutations. The aim of the study was to assess the type of mutations in patients, clinically diagnosed with FH in Singapore. METHODS: Patients (probands) with untreated/highest on-treatment LDL-c>4...
December 27, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/29353061/next-generation-sequencing-to-detect-deletion-of-rb1-and-erbb4-genes-in-chromophobe-renal-cell-carcinoma-a-potential-role-in-distinguishing-chromophobe-renal-cell-carcinoma-from-renal-oncocytoma
#3
Qingqing Liu, Kristine M Cornejo, Liang Cheng, Lloyd Hutchinson, Mingsheng Wang, Shaobo Zhang, Keith Tomaszewicz, Ediz F Cosar, Bruce A Woda, Zhong Jiang
Overlapping morphological, immunohistochemical, and ultrastructural features make it difficult to diagnose chromophobe renal cell carcinoma (ChRCC) and renal oncocytoma (RO). Since ChRCC is a malignant tumor, whereas RO is a tumor with benign behavior, it is important to distinguish these two entities. We aimed to identify genetic markers that distinguish ChRCC from RO by using next-generation sequencing (NGS). NGS for hotspot mutations or gene copy number changes was performed on 12 renal neoplasms including seven ChRCC and five RO cases...
January 15, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29352613/mrna-translation-gone-awry-translation-fidelity-and-neurological-disease
#4
REVIEW
Mridu Kapur, Susan L Ackerman
Errors during mRNA translation can lead to a reduction in the levels of functional proteins and an increase in deleterious molecules. Advances in next-generation sequencing have led to the discovery of rare genetic disorders, many caused by mutations in genes encoding the mRNA translation machinery, as well as to a better understanding of translational dynamics through ribosome profiling. We discuss here multiple neurological disorders that are linked to errors in tRNA aminoacylation and ribosome decoding. We draw on studies from genetic models, including yeast and mice, to enhance our understanding of the translational defects observed in these diseases...
January 15, 2018: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/29352504/trophic-niche-capture-efficiency-and-venom-profiles-of-six-sympatric-ant-eating-spider-species-araneae-zodariidae
#5
Stano Pekár, Lenka Petráková, Ondrej Šedo, Stanislav Korenko, Zbyněk Zdráhal
The arms race between specialist predators and their prey has resulted in the evolution of a variety of specific adaptations. In venomous predators this can include venom composition, particularly if predators are specialised on dangerous prey. Here, we performed an integrative study using six species of highly specialised ant-eating spiders of the genus Zodarion in order to investigate their phylogeny, realised trophic niche, efficacy in the capture of various ant species, and venom composition. Data on natural diet obtained by next-generation sequencing and field observations showed that the six Zodarion species exploit different ant species...
January 19, 2018: Molecular Ecology
https://www.readbyqxmd.com/read/29352324/efficient-genome-wide-genotyping-strategies-and-data-integration-in-crop-plants
#6
REVIEW
Davoud Torkamaneh, Brian Boyle, François Belzile
Next-generation sequencing (NGS) has revolutionized plant and animal research by providing powerful genotyping methods. This review describes and discusses the advantages, challenges and, most importantly, solutions to facilitate data processing, the handling of missing data, and cross-platform data integration. Next-generation sequencing technologies provide powerful and flexible genotyping methods to plant breeders and researchers. These methods offer a wide range of applications from genome-wide analysis to routine screening with a high level of accuracy and reproducibility...
January 19, 2018: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/29351890/evolutionary-mechanisms-studied-through-protein-fitness-landscapes
#7
REVIEW
Aneth S Canale, Pamela A Cote-Hammarlof, Julia M Flynn, Daniel Na Bolon
Biology has, and continues to be, shaped by evolutionary mechanisms. Within the past decade, local fitness landscapes have become experimentally tractable and are providing new perspectives on evolutionary mechanisms. Powered by next-generation sequencing, the impacts of all individual amino acid substitutions on function have been quantified for dozens of proteins. These fitness maps have been utilized to investigate the biophysical underpinnings of existing protein function as well as the appearance and enhancement of new protein functions...
January 16, 2018: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/29351737/identifying-genome-wide-immune-gene-variation-underlying-infectious-disease-in-wildlife-populations-a-next-generation-sequencing-approach-in-the-gopher-tortoise
#8
Jean P Elbers, Mary B Brown, Sabrina S Taylor
BACKGROUND: Infectious disease is the single greatest threat to taxa such as amphibians (chytrid fungus), bats (white nose syndrome), Tasmanian devils (devil facial tumor disease), and black-footed ferrets (canine distemper virus, plague). Although understanding the genetic basis to disease susceptibility is important for the long-term persistence of these groups, most research has been limited to major-histocompatibility and Toll-like receptor genes. To better understand the genetic basis of infectious disease susceptibility in a species of conservation concern, we sequenced all known/predicted immune response genes (i...
January 19, 2018: BMC Genomics
https://www.readbyqxmd.com/read/29351563/a-consensus-linkage-map-of-lentil-based-on-dart-markers-from-three-ril-mapping-populations
#9
Duygu Ates, Secil Aldemir, Ahmad Alsaleh, Semih Erdogmus, Seda Nemli, Abdullah Kahriman, Hakan Ozkan, Albert Vandenberg, Bahattin Tanyolac
BACKGROUND: Lentil (Lens culinaris ssp. culinaris Medikus) is a diploid (2n = 2x = 14), self-pollinating grain legume with a haploid genome size of about 4 Gbp and is grown throughout the world with current annual production of 4.9 million tonnes. MATERIALS AND METHODS: A consensus map of lentil (Lens culinaris ssp. culinaris Medikus) was constructed using three different lentils recombinant inbred line (RIL) populations, including "CDC Redberry" x "ILL7502" (LR8), "ILL8006" x "CDC Milestone" (LR11) and "PI320937" x "Eston" (LR39)...
2018: PloS One
https://www.readbyqxmd.com/read/29350590/human-genetics-and-molecular-mechanisms-of-vein-of-galen-malformation
#10
Daniel Duran, Philipp Karschnia, Jonathan R Gaillard, Jason K Karimy, Mark W Youngblood, Michael L DiLuna, Charles C Matouk, Beverly Aagaard-Kienitz, Edward R Smith, Darren B Orbach, Georges Rodesch, Alejandro Berenstein, Murat Gunel, Kristopher T Kahle
Vein of Galen malformations (VOGMs) are rare developmental cerebrovascular lesions characterized by fistulas between the choroidal circulation and the median prosencephalic vein. Although the treatment of VOGMs has greatly benefited from advances in endovascular therapy, including technical innovation in interventional neuroradiology, many patients are recalcitrant to procedural intervention or lack accessibility to specialized care centers, highlighting the need for improved screening, diagnostics, and therapeutics...
January 19, 2018: Journal of Neurosurgery. Pediatrics
https://www.readbyqxmd.com/read/29350137/multiplex-pcr-based-next-generation-sequencing-and-global-diversity-of-seoul-virus-in-humans-and-rats
#11
Won-Keun Kim, Jin Sun No, Seung-Ho Lee, Dong Hyun Song, Daesang Lee, Jeong-Ah Kim, Se Hun Gu, Sunhye Park, Seong Tae Jeong, Heung-Chul Kim, Terry A Klein, Michael R Wiley, Gustavo Palacios, Jin-Won Song
Seoul virus (SEOV) poses a worldwide public health threat. This virus, which is harbored by Rattus norvegicus and R. rattus rats, is the causative agent of hemorrhagic fever with renal syndrome (HFRS) in humans, which has been reported in Asia, Europe, the Americas, and Africa. Defining SEOV genome sequences plays a critical role in development of preventive and therapeutic strategies against the unique worldwide hantavirus. We applied multiplex PCR-based next-generation sequencing to obtain SEOV genome sequences from clinical and reservoir host specimens...
February 2018: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29349761/multi-gene-panel-testing-in-breast-cancer-management
#12
Christos Fountzilas, Virginia G Kaklamani
Hereditary predisposition accounts for approximately 10% of all breast cancers and is mostly associated with germline mutations in high-penetrance genes encoding for proteins participating in DNA repair through homologous recombination (BRCA1 and BRCA2). With the advent of massive parallel next-generation DNA sequencing, simultaneous analysis of multiple genes with a short turnaround time and at a low cost has become possible. The clinical validity and utility of multi-gene panel testing is getting better characterized as more data on the significance of moderate-penetrance genes are collected from large, cancer genetic testing studies...
2018: Cancer Treatment and Research
https://www.readbyqxmd.com/read/29349441/association-between-sn-2-fatty-acid-profiles-of-breast-milk-and-development-of-the-infant-intestinal-microbiome
#13
Tiemin Jiang, Bin Liu, Jufang Li, Xueyan Dong, Man Lin, Minghui Zhang, Junying Zhao, Yaohua Dai, Lijun Chen
Increasing evidence shows that host diet and gut microbes are related. Previous studies have shown the effects of specific dietary fatty acids (FAs) on intestinal microbiota, but little is known about the effect of the stereospecifically numbered sn-2 position in triglycerides (TG) of human milk on the gut microbiome of infants. This study aimed at examining possible effects of sn-2 FAs of human milk on the gut microbial development of breastfeeding babies. Sn-2 FAs and intestinal microbiota were assessed by GC-MS and high-throughput 16S rRNA sequencing, respectively...
January 19, 2018: Food & Function
https://www.readbyqxmd.com/read/29349042/an-optimized-targeted-next-generation-sequencing-approach-for-sensitive-detection-of-single-nucleotide-variants
#14
S Stasik, C Schuster, C Ortlepp, U Platzbecker, M Bornhäuser, J Schetelig, G Ehninger, G Folprecht, C Thiede
Monitoring of minimal residual disease (MRD) has become an important clinical aspect for early relapse detection during follow-up care after cancer treatment. Still, the sensitive detection of single base pair point mutations via Next-Generation Sequencing (NGS) is hampered mainly due to high substitution error rates. We evaluated the use of NGS for the detection of low-level variants on an Ion Torrent PGM system. As a model case we used the c.1849G > T (p.Val617Phe) mutation of the JAK2-gene. Several reaction parameters (e...
May 2018: Biomolecular Detection and Quantification
https://www.readbyqxmd.com/read/29348906/an-ank1-ivs3-2a-c-mutation-causes-exon-4-skipping-in-two-patients-from-a-chinese-family-with-hereditary-spherocytosis
#15
Xiong Wang, Liyan Mao, Na Shen, Jing Peng, Yaowu Zhu, Qun Hu, Yanjun Lu
Hereditary spherocytosis (HS) is a congenital hemolytic anemia that affects the cell membrane of red blood cells and is characterized by the presence of spherical-shaped erythrocytes in the peripheral blood film. The clinical manifestation of HS ranges from asymptomatic to severe cases that require transfusion during early childhood. HS is caused by mutations in red blood cell membrane protein encoding genes, including ANK1, EPB42, SLC4A1, SPTA1, and SPTB. Mutations of the ANK1 gene account for 75% of all HS cases, and these particular mutations are typically inherited in an autosomal dominant manner...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348827/molecular-genetic-profiling-and-high-throughput-in-vitro-drug-screening-in-nut-midline-carcinoma-an-aggressive-and-fatal-disease
#16
Anja Stirnweiss, Joyce Oommen, Rishi S Kotecha, Ursula R Kees, Alex H Beesley
NUT midline carcinoma (NMC) is a rare and aggressive cancer, with survival typically less than seven months, that can arise in people of any age. Genetically, NMC is defined by the chromosomal fusion of NUTM1 with a chromatin-binding partner, typically the bromodomain-containing protein BRD4. However, little is known about other genetic aberrations in this disease. In this study, we used a unique panel of cell lines to describe the molecular-genetic features of NMC. Next-generation sequencing identified a recurring high-impact mutation in the DNA-helicase gene RECQL5 in 75% of lines studied, and biological signals from mutation-signature and network analyses consistent with a general failure in DNA-repair...
December 22, 2017: Oncotarget
https://www.readbyqxmd.com/read/29348353/next-generation-sequencing-reveals-the-first-complete-genome-sequence-of-cowpea-aphid-borne-mosaic-virus-from-uganda
#17
E K Mbeyagala, P Tukamuhabwa, J Bisikwa, T Holton, S B Mukasa
We present here the first complete genome sequence of Cowpea aphid-borne mosaic virus (CABMV) isolated from cowpea in Uganda and compare it with five CABMV complete genome sequences from Brazil (2), India (2), and Zimbabwe (1). It most resembled the genomes of two Brazilian isolates (MG-Avr and BR1) and one Indian isolate (RR3).
January 18, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29348316/evaluation-of-next-generation-anti-cd20-antibodies-labeled-with-zirconium-89-in-human-lymphoma-xenografts
#18
Jason T Yoon, Mark S Longtine, Bernadette V Marquez-Nostra, Richard L Wahl
Radioimmunotherapies with monoclonal antibodies (mAbs) to the B-lymphocyte antigen 20 (CD20) are effective treatments for B-cell lymphomas, but United States Food and Drug Administration (FDA)-approved radioimmunotherapies exclusively use radiolabeled murine antibodies, potentially limiting re-dosing. The FDA recently approved two unlabeled anti-CD20 monoclonal antibodies, obinutizumab and ofatumumab, termed "next generation" as they are humanized (obinituzumab) or fully human (ofatumumab), thus potentially allowing a greater potential for re-dosing than with previous generation anti-CD20 antibodies, including rituximab (chimeric) and tositumumab (murine) which contain more murine peptide sequences...
January 18, 2018: Journal of Nuclear Medicine: Official Publication, Society of Nuclear Medicine
https://www.readbyqxmd.com/read/29348113/genetics-in-endocrinology-the-expanding-genetic-horizon-of-primary-aldosteronism
#19
Silvia Monticone, Fabrizio Buffolo, Martina Tetti, Franco Veglio, Barbara Pasini, Paolo Mulatero
Aldosterone is the main mineralocorticoid hormone in humans and plays a key role in maintaining water and electrolyte homeostasis. Primary aldosteronism (PA), characterized by autonomous aldosterone overproduction by the adrenal glands, affects 6% of the general hypertensive population and can be either sporadic or familial. Aldosterone producing adenoma (APA) and bilateral adrenal hyperplasia (BAH) are the two most frequent subtypes of sporadic PA, and 4 forms of familial hyperaldosteronism (FH-I to FH-IV) have been identified...
January 18, 2018: European Journal of Endocrinology
https://www.readbyqxmd.com/read/29347911/micrornas-associated-with-early-neural-crest-development-in-xenopus-laevis
#20
Nicole J Ward, Darrell Green, Janet Higgins, Tamas Dalmay, Andrea Münsterberg, Simon Moxon, Grant N Wheeler
BACKGROUND: The neural crest (NC) is a class of transitory stem cell-like cells unique to vertebrate embryos. NC cells arise within the dorsal neural tube where they undergo an epithelial to mesenchymal transition in order to migrate and differentiate throughout the developing embryo. The derivative cell types give rise to multiple tissues, including the craniofacial skeleton, peripheral nervous system and skin pigment cells. Several well-studied gene regulatory networks underpin NC development, which when disrupted can lead to various neurocristopathies such as craniofrontonasal dysplasia, DiGeorge syndrome and some forms of cancer...
January 18, 2018: BMC Genomics
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